metadata_file: The Metadata File

In bpollner/aquap2: Multivariate Data Analysis Tools for R including Aquaphotomics Methods

The Metadata File

Description

The metadata file contains all the metadata of an experiment like experiment name etc. It is also used to design the experiment and to export a randomized sample list that then can be used in the data acquisition process. Additionally, the references to the temperature calibration file (necessary for plotting Aquagrams) and to the file containing the noise-spectra are kept here.

Arguments

expName	The name of the experiment. This will be used in many plot titles and as a first part of the name of saved PDFs.
commonValue	Character. A value that will be be present in all the rows of the dataset. The default 'def' reads in the default value from the settings.r file. (Parameter p_commonNoSplit.)
envControlLabel	The label for the environmental control. Leave at def to take the default value from the settings (parameter p_envControlLabel).
realMeasurementLabel	The label for the "real measurement", for all the samples of an experiment. Leave at def to take the default value from the settings (parameter p_realMeasurementLabel).
xaxDenominator	The unit that is displayed on the x-axis when plotting e.g. raw spectra.
yaxDenominator	The unit that is displayed on the y-axis when plotting e.g. raw spectra.
TimePoints	Logical 'FALSE' or a character vector. Leave at 'FALSE' if your experiment does not cover more than one point in time, otherwise provide a label for each time-point in the format c("T0", "T1", "T2", ...) or leave at 'FALSE' for no time-splitting.
nrConScans	Numeric length one. The number of consecutive scans for each sample.
spacing	Numeric length one. The number of "real measurements" between each "environmental control", i.e. the "space" between environmental control samples (set to FALSE for not inserting environmental controls).
sl_classes	Character length one. The name of the xlsx file located in the metadata folder holding the desired class structure for the experiment, see details.
Repls	Numeric. How many replicates of each sample to measure. The values in the dataset wil be prefixed with the default character for the replicates, which can be set in the settings (default is "R"). So, with e.g. three replicates you will find the values "R1", "R2", and "R3" in the dataset.
Group	Character vector. Additional groups to split the above generated classes into, like e.g. experiment and control. Please see details.
filetype	Character length one. The filetype of the raw-data file. Leave at def to get the default from the settings (parameter imp_specFileType). If a value other than def is provided in the argument filetype in getFullData, this is overriding the value of filetype in the metadata file. Please refer to getFullData for possible values.
noiseFileName	The name of the corresponding noise-data file residing in the AQUAP2SH folder. Leave at def to get the default from the settings (parameter noi_noiseDataFilename. If a value other than def is provided in the argument noiseFile in the function gdmm, this is overriding the value of 'noiseFileName' here in the metadata file. Please refer to noise_procedures for more information.
tempCalibFileName	The name of the corresponding temperature-data file residing in the AQUAP2SH folder. Leave at def to get the default from the settings (parameter aqg_tempCalib_Filename). If a value other than def is provided in the argument tempFile in the function gdmm, this is overriding the value of tempCalibFileNamehere in the metadata file. Please refer to tempCalib_procedures for more information.
sampleListType	The type of sample-list file in the sampleLists/sl_in folder. Leave at def to get the default from the settings (parameter imp_sampleListType). If a value other than def is provided in the argument slType in the function getFullData, this is overriding the value of sampleListType in the metadata file. Please refer to getFullData for possible values.
tempHumLog	If data from temperature and rel.humidity logger should be imported and aligned to a timestamp in the dataset. Leave at def to get the default from the settings (parameter imp_use_TRH_logfile). If a value other than def is provided in the argument trhLog in the function getFullData, this is overriding the value of tempHumLog in the metadata file. Please refer to getFullData for possible values.
multiplyRows	Character def or Logical. If all the rows in the sample list should be multiplied by the number of consecutive scans as specified in the metadata of the experiment. Leave at def to get the default from the settings (parameter imp_multiplyRows). If a value other than def is provided in the argument multiplyRows in the function getFullData, this is overriding the value of multiplyRows in the metadata file. Please refer to getFullData for possible values.

Details

While the parameters TimePoints, nrConScans, spacing, Repls and Group can be used to further modify an existing sample list, the class structure as provided in the Excel file referenced at argument sl_classes is defining the basic class-structure of an experiment. Please refer to XXX for examples on how define the class structure via xlsx-input.

See Also

getmd

Other fileDocs: anproc_file, settings_file

bpollner/aquap2 documentation built on March 29, 2024, 7:33 a.m.